Circularization of linear nucleic acid molecules often requires enzymatic steps. One alternative to circularizing linear DNA molecules is by site-specific recombination. A number of approaches for the joining of DNA molecules have been described using the Cre-loxP site-specific recombination system, including Sauer and Henderson, (1988), Gene 70, 331-341; WO 00/26396; WO 02/083889; and U.S. Pat. App. No. 2004/0092016.